Wednesday, July 31, 2013

OMG

Because when people as smart as Dan Graur believe in scientifically impossible fables of spontaneous origins there’s got to be a reason. And that reason is, of course, religion, or more politely, metaphysics, which has been commandeering science for centuries and no less so today. That is why Dan Graur’s non scientific Slide 18 in his talk at the Annual Meeting of the Society for Molecular Biology and Evolution this month—the only slide that really mattered—was not met with gasps in Chicago, but with chuckles. As Paul warned Timothy, “For the time will come when they will not endure sound doctrine, but according to their own desires, because they have itching ears, they will heap up for themselves teachers; and they will turn their ears away from the truth, and be turned aside to fables.”

Tuesday, July 30, 2013

It Will Only Get Bigger

Animal groups do not evolve greater and greater new designs as time goes by, but rather are at their maximum level of diversity early in their history. And species must be constrained in how much they can change. The ignorant babblings of creationists? Ridiculous criticisms of IDs? True they have been making such claims for years, but this time it comes from evolutionists at the University of Bath who performed a massive fossil study. As one of the evolutionists explained:

This pattern, known as “early high disparity,” turns the traditional V-shaped cone model of evolution on its head. What is equally surprising in our findings is that groups of animals are likely to show early-high disparity regardless of when they originated over the last half a billion years.

Early high disparity? And another one of the evolutionists explained that species must be constrained in how much they can change:

Our work implies that there must be constraints on the range of forms within animal groups, and that these limits are often hit relatively early on. The only exceptions to the rule are groups that were wiped out at times of mass extinction.

In their paper they explained that there are few putative macroevolutionary trends or rules that withstand scrutiny. Funny, we’ve been saying that for years. The difference is we don’t carry a theological mandate for evolution.

Now we find such talk in evolution papers. These findings join the thousands of other scientific problems with evolution, slowly eating away at the foundation.

Monday, July 29, 2013

“A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”—Max Planck

Evolutionists will never “see the light,” as Max Planck put it, no matter how badly their theory fares, because evolution is not an ordinary scientific theory. Evolution is not believed to be true because of scientific evidence that the species arose via random events and natural law—chance and necessity—but because the anti thesis, design and creation, has been refuted. Indeed, the idea that the biological world spontaneously arose is scientifically unlikely. But it must be true because, as evolutionists explain, creationism is obviously false. As the leading twentieth century evolutionist, Ernst Mayr, once explained, evolution achieved its predominance “less by the amount of irrefutable proofs it has been able to present than by the default of all the opposing theories.” But those opposing theories were refuted on the basis of religious claims. As Stephen Gould put it:

Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense.

Likewise Jerry Coyne explains that the appearance of species through time is “far from random” and “no theory of special creation, or any theory other than evolution, can explain these patterns.” [29] And why are species so similar? “There is no reason,” explains Coyne, “why a celestial designer, fashioning organisms from scratch like an architect designs buildings, should make new species by remodeling the features of existing ones.” [54]

No reason? How does Coyne know that?

Another favorite source of proof for evolution is embryology. Here are representative quotes from leading evolutionists:

How does God’s plan for humans and sharks require them to have almost identical embryos? [Douglas Futuyma, Science on Trial: The Case for Evolution, p. 48]

The passage through a fishlike stage by the embryos of the higher vertebrates is not explained by creation, but is readily accounted for as an evolutionary relic. [Tim Berra, Evolution and the Myth of Creationism, p. 22]

Now, we’re not absolutely sure why some species retain much of their evolutionary history during development. The “adding new stuff onto old” principle is just a hypothesis—and explanation for the facts of embryology. It’s hard to prove that it was easier for a developmental program to evolve one way rather than another. But the facts of embryology remain, and make sense only in light of evolution. [Jerry Coyne, Why Evolution is True, p. 78-9]

Of course these claims about creationism and precisely what God would and would not do, are not from science. Nor are the many other metaphysical claims that, over and over, prove evolution.

In fact evolution is drenched in metaphysics. From its early formulations in the Enlightenment years, to Darwin, to today’s refinements, evolution relies on non scientific assumptions. The “fact” of evolution has never been demonstrated without appeal to non scientific truths.

This reasoning is perfectly valid but it is metaphysical—it is based on our definition of a “sensible God.” So while the empirical science reveals the details of why evolution is unlikely, the religious sentiment mandates that evolution is, somehow, true because creationism must be false.

This reliance on the refutation of creationism means that evolution is a religious theory. But some evolutionists deny this. Yes we say creationism has failed, but that doesn’t make evolution religious, explain these evolutionists. One can test the claims of a theory without agreeing or believing in the premises and beliefs of that theory.

The problem is they are not merely testing the claims of creationism. That is a canard that makes no sense. For centuries evolutionists have fervently expounded that God would not have created such a world as this one. This is no academic, dispassionate analysis. In fact most of the evolutionists claims about creationism would not be recognized by most creationists or design advocates.

Evolutionists are not testing the claims of creationism, they are proclaiming their religious beliefs about God and creation. Beliefs that they have proclaimed for centuries.

Imagine if evolutionists were indeed merely testing some claims they had found in their favorite creationist journal. If that were actually the case, then the most evolutionists could claim is that they have falsified a particular theory of creationism. They would not be able to conclude that evolution is the only remaining alternative. There are many, many potential theories of creationism. They would have refuted only one of them and this would tell us very little about evolution. There would be one less competitor, but the monumental scientific problems with evolution would remain. And so would all but one of the competing theories.

The giveaway is in the takeaway. You can tell how serious evolutionists are about their religious premises by their conclusion that evolution must be true. Or in other words, evolutionists can only conclude that evolution is a fact if they are not merely testing a particular form of creationism, but rather are testing universal claims about creationism.

Their conclusion that evolution is a fact means they believe their claims about creationism are universal. For example, Coyne really believes that God would never have created species with the similarities that we find or the embryonic stages we observe.

As Coyne says, no theory other than evolution can explain these patterns. How can Coyne have knowledge about all possible explanations? The answer, of course, is that he cannot have such knowledge. At least not from science. That kind of knowledge only comes from religion.

Saturday, July 27, 2013

There’s More to the Story, Much More

Imagine that you saw a magnificent mansion and when you asked where it came from, you were shown a box of fantastic tools. Perhaps those fantastic tools were used to construct the mansion, but they don’t exactly answer your question. What about the construction materials, the workers, the design, and the construction process? Those unanswered questions are like the recent findings of how squids and octopuses control their image and color. Action potentials travel down the nerve to the synapse near the skin of the squid or octopus, the neurotransmitter acetylcholine is released and it sets off a sequence of events in special cells. Special proteins are phosphorylated, they congregate, the cell membrane folds in on itself, water is transported, the cell’s osmotic pressure shifts and its refractive index is adjusted to cause a change in the reflected light. In short, it changes color.

Those are a fantastic set of tools, but they leave many questions unanswered if we’re wondering how the squid changes it color. Just for starters, how did the correct action potentials, at the right time, in the right nerve cells, become activated?

No, I’m not asking how action potentials are physically initiated. That’s a fascinating story in itself, but it is just another tool. What I’m asking is, how was it decided when and where to set off action potentials?

Somehow there must be the correct neural processing that takes as input the environmental situation or challenge, interprets that information, and formulates the appropriate neuron firing strategy. That is yet another layer of complexity on the squid and octopus coloration story.

As unlikely as evolution is when considering the tools of coloration control, its astronomically low probability takes another plunge when we add this neural processing requirement. It is yet another reason why the “evolution is a fact” claim does not come from science.

Another Astonishing Design

We have discussed some amazing examples of how species control their color (here and here, for example) and how such technology in nature has inspired engineers creating advanced new technologies such as low-power video displays. Now new research is helping to explain how squids and octopuses change color and it is amazing.

We usually think of color as resulting from chemistry, such as in dyes. But different colors can also result from repeating, detailed submicron geometrical structures at the object’s surface. The new research reveals yet another, even more complex system for manipulating the frequency of light (i.e., the color) coming from squids and octopuses.

It begins with nerve signals which are sent to special cells containing special proteins. The signal causes the proteins to congregate and deep pleats to form in the cell membrane, altering the osmotic pressure and ultimately its refractive index.

Initially, before the proteins are consolidated, the refractive index -- you can think of it as the density -- inside the lamellae and outside, which is really the outside water environment, is the same. There's no optical difference so there's no reflection. But when the proteins consolidate, this increases the refractive index so the contrast between the inside and outside suddenly increases, causing the stack of lamellae to become reflective, while at the same time they dehydrate and shrink, which causes color changes. The animal can control the extent to which this happens -- it can pick the color -- and it's also reversible. The precision of this tuning by regulating the nanoscale dimensions of the lamellae is amazing.

Squids have used their tunable iridescence for camouflage and communication for millions of years; materials scientists have more recently looked to them for inspiration to develop new “biologically inspired” adaptive optics. Iridocyte cells produce iridescence through constructive interference of light with intracellular Bragg reflectors. The cell’s dynamic control over the apparent lattice constant and dielectric contrast of these multilayer stacks yields the corresponding optical control of brightness and color across the visible spectrum. Here, we resolve remaining uncertainties in iridocyte cell structure and determine how this unusual morphology enables the cell’s tunable reflectance. We show that the plasma membrane periodically invaginates deep into the iridocyte to form a potential Bragg reflector consisting of an array of narrow, parallel channels that segregate the resulting high refractive index, cytoplasmic protein-containing lamellae from the low-index channels that are continuous with the extracellular space. In response to control by a neurotransmitter, the iridocytes reversibly imbibe or expel water commensurate with changes in reflection intensity and wavelength. These results allow us to propose a comprehensive mechanism of adaptive iridescence in these cells from stimulation to color production. Applications of these findings may contribute to the development of unique classes of tunable photonic materials.

What we see here is a beautiful design consisting of a sequence of highly complex, intricate and finely-tuned mechanisms, molecules and structures allowing these organisms to precisely control their image. There is no scientific evidence that such optical technology arose from random mutations as evolutionists believe. Evolutionists like to call upon natural selection as a sort of natural designer, but that does not help for such intricate designs as these.

Thursday, July 25, 2013

What Goes Around Comes Around

Think evolution’s idea of random changes occurring spontaneously and experimenting with all manner of combinations to construct the biological world is a revolutionary, unprecedented finding of modern science? Then you might want to read up on Lucretius who wrote two thousand years ago that, among other things:

But because throughout the universe from time everlasting countless numbers of [atoms], buffeted and impelled by blows, have shifted in countless ways, experimentation with every kind of movement and combination has at last resulted in arrangements such as those that created and compose our world.

Of course the fact is that from antiquity to today, we have been saying pretty much the same thing, and building the same tower, over and over. For not only did Lucretius get the random movements and combinations part right, he also got the motivation right:

That in no wise the nature of all things
For us was fashioned by a power divine-So great the faults it stands encumbered with.

Fast forward two thousand years to the brand new idea of evolution:

Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history, follows perforce. No one understood this better than Darwin. Ernst Mayr has shown how Darwin, in defending evolution, consistently turned to organic parts and geographic distributions that make the least sense. [Stephen J. Gould, 1980]

It has been the same story all along. This world is faulty, therefore no designer ever would have designed it, and therefore it must have evolved spontaneously. These ground rules come from the metaphysics and the details are left for the science.

Wednesday, July 24, 2013

Who Will Tell the People?

No sooner had we pointed out that while, as Andreas Wagner admitted, we know “very little” about how evolutionary innovations originate and that “Exactly how new traits emerge is a question that has long puzzled evolutionary biologists,” such inconvenient truths are rarely admitted in public, then leading science writer Carl Zimmer, as if on cue, writing for Scientific American on the topic of “how organisms can evolve elaborate structures,” informed his readers that when it comes to complexity “To some extent, it just happens,” and that “intricate systems of proteins can evolve from simpler ones,” and finally that “studies suggest” that random mutations “can fuel the emergence of complexity.”

That incredible sequence of whoppers makes us wonder, why is it that we cannot simply tell the truth about the science? Who will tell the people?

Tuesday, July 16, 2013

Evolution’s Serendipity Just Went Ballistic

It was not news this week when evolutionist Andreas Wagner explained that “we know very little about how they [evolutionary innovations] originate.” The origin of evolutionary innovations is largely unexplained and that gap is well known. No one would deny this. Even Wagner’s own press release begins with the same admission: “Exactly how new traits emerge is a question that has long puzzled evolutionary biologists.” But this admission, while uncontroversial, is not well advertised. It is not typically found in textbooks or popular books. Evolutionists do not often discuss this shortcoming in their class lectures or public talks. For this shortcoming is rather embarrassing. In order to be taken seriously evolution must be able to explain how life’s various and incredible innovations arose, and it hasn’t been able to do that. This raises two interesting tensions for evolutionists.

The most obvious tension raised by evolution’s inability to explain the origin of innovations is that it undercuts the evolutionist’s claim that evolution is a fact. The origin of innovations is one of those fundamental problems. It is not a minor side issue that can be delegated to future research or assigned to the student. If evolution cannot explain that, then it fails. So far evolution has not been able to explain this difficult problem. But how then can evolution be a fact?

The answer is that the “fact” of evolution does not derive from the scientific evidence. Evolution is assumed from the beginning. It is a given. It is the paradigm in which evolutionists work and not vulnerable to empirical science. How evolution is supposed to have worked is very much open to scientific research. But whether or not evolution actually created the entire biological world is not open to scientific research. It is not falsifiable, for it is taken to be true. Evolutionists are constantly questioning the various ideas of how evolution worked (because there are substantial problems with those ideas), but evolutionists never question the fact of evolution.

How evolution created all those innovations is largely unexplained, but evolutionists never question the fact of evolution. And they even claim it comes from science.

The second tension arises from how evolutionists have attempted to explain life’s incredible mechanisms and machines. Such machines are not likely to be created by blind natural laws--they require forward-looking thought. Assembly is required, and there is no payback until the final step. Evolution’s natural selection will not do the job because the machine does not help the organism until the machine is complete. Natural selection lacks the foresight required to construct such machines.

An unlikely way around this barrier is to have the different parts of the machine evolve independently, for their own purposes or perhaps for no purpose at all. Later, the parts come together to form a super machine. In other words, each part of the super machine evolves on its own, in a neutral fashion or to perform its own function. Then, serendipitously, the different machines just happen to fit together and perform a new function. Imagine a fuselage and a pair of wings uniting to form an aircraft.

This rather heroic explanation is called preadaptation or exaptation, and evolutionists have relied rather heavily on it to explain biology's complexities. But Wagner and coworkers are now raising this to a new level. They say these exaptations are the rule in evolution’s history of creating wonders. As Wagner explained this week, “Our work shows that exaptations exceed adaptations several-fold.”

Or as one headline succinctly put it, “Most Traits Emerge for No Crucial Reason, Scientists Find.”

When an investment goes bad sometimes it is best to take the loss and be done with it. No sense in throwing good money after bad. This exaptation explanation does not save the theory. No, Wagner and co-workers did not “find” that most traits emerge from exaptations, as the headline above states.

Not in a scientific way at least. You see they first assumed evolution is true. Only on the shoulders of that heroic assumption did they arrive at the exaptation explanation.

From a strictly scientific perspective, the exaptation explanation does not work. For it requires that evolution is constantly getting lucky as it constructs all kinds of biological subcomponents and machines which, as luck would have it, just happen to fit together to form completely new and different machines which work wonders.

So the second tension is that explanations that evolutionists do come up with to explain the origin of innovations just make matters worse. For they reveal how badly evolution fares in light of the evidence.

Monday, July 15, 2013

But Evolution is a Fact

When Charles Darwin presented his theory of evolution in 1859 it received instant approval. Darwin’s tome was the perfect creation narrative for a culture and a clergy that viewed the creator as more eminent than immanent. Like Aristotle’s Unmoved Mover, the creator was exalted as transcendent, and so safely sequestered away from the details of this world which he should be neither aware of nor responsible for. A decade earlier John Millais discovered all of this the hard way when Charles Dickens, as just one example, scathingly criticized the young prodigy’s Christ in the House of His Parents (shown above) for its portrayal of the subject as a “hideous, wry-necked, blubbering, red-headed boy, in a bed-gown.” Another critic lamented the painting’s “studious vulgarity of portraying the youthful Saviour as a red-headed Jew boy.” Millais had presented a decidedly immanent deity that did not comport well with the Gnosticism of the day. Darwin, on the other hand, had been concerned for decades about how the creator should be juxtaposed against the various inefficient, ignoble or downright evil aspects of nature that he and others were uncovering. Do you believe “the shape of my nose was designed?” Darwin asked his friend Charles Lyell. If Lyell did think so then, Darwin added, “I have nothing more to say.” This ancient sentiment that our spiritual God should have little or nothing to do with this material world was more than just popular in Darwin’s day. It dictated what was acceptable and unacceptable in the arts and sciences. But what about the empirical evidence?

While Darwin’s theory of evolution followed the cultural norms, the idea that the most complex things known arose via random events and natural law did not seem scientifically feasible. Do we really live in a universe in which complex, interdependent, fine-tuned mechanisms and structures just happen to arise by themselves? This has always been the main problem with evolution.

Evolution is a fact, not because of the science, but because of the metaphysics. We don’t know evolution is true because the science just makes it so obvious. Quite the opposite, as evolutionist Andreas Wagner explains this week, “we know very little about how they [evolutionary innovations] originate.”

We know very little about how evolutionary innovations originate? But that is the main sticking point. How can we then say evolution is a fact? It would be like claiming perpetual motion is a fact, though we haven’t demonstrated it and don’t yet know how it could work.

The answer, of course, is that evolution is a fact because evolution must be a fact. Until and unless we understand its complex intertwining of theology and science, we won’t understand this thing we call evolution.

Saturday, July 13, 2013

Evolution is Getting Demolished

No sooner had Dan Graur finished his talk at the Annual Meeting of the Society for Molecular Biology and Evolution this week on how if ENCODE’s conclusion (that much of our genome is functional rather than junk) is true, then evolution is false, but that ENCODE most assuredly is not true, that the human genome is small, low on genes, unoriginal and repetitive, and that junk DNA is a known known, then new research out of John Mattick’s lab took the next step in the inexorable march of science showing that, once again, it’s not good to bet against Mother Nature. While Graur argued that only about 5% of our genome can be functional because, after all, the pufferfish’s genome is way larger than ours and we surely we can’t believe in human exceptionalism and Goldilockism (which certainly got some laughs in Chicago), Mattick and crew reported on actual experiments suggesting that, err, “a large proportion of the mammalian genome is functional.”

The Mattick results show that in addition to the 5-8% of the genome with conserved DNA sequence, a much higher percentage, possibly up to 30%, has conserved RNA structure. You see while protein structure is difficult to predict from the amino acid sequence, RNA structure can be predicted relatively accurately from the nucleotide sequence. So the new research from Mattick’s lab computed the predicted RNA structures from dozens of mammalian genomes and searched for conserved structures across the different species.

A conserved structure across multiple species, according to evolution, probably has been conserved by purefying selection. In other words, it contributes to the organism’s fitness, and so has function and is not junk.

The bottom line is while ENCODE found that more than three-quarters of our genome is transcribed, which is circumstantial evidence for function, Mattick’s lab is now providing even stronger evidence for function for about a third of that three-quarters of our genome.

And that additional evidence was obtained only using a particular method. There are many, many more potential lines of inquiry that could show more genome function. In other words, that 30% figure is only going to grow.

In fact it already is larger when you consider other work, such as the recent findings that the so-called Alu elements “have been shown to control mRNA processing at several levels, to have complex regulatory functions such as transcriptional repression and modulating alternative splicing and to cause a host of human genetic diseases.”

Perhaps our prediction, that Graur’s claim (that if ENCODE is true then evolution must be false) will be conveniently ignored and forgotten, will come true sooner rather than later. For none of this will change evolutionary thought. No matter how ridiculous the data shows evolution to be, the truth status of evolution never was and never will be vulnerable to scientific evidence.

Friday, July 12, 2013

But There is One Glaring Error

Evolution has always had a love-hate relationship with biological junk. When scientists discover something new in biology but don’t understand it, evolutionists—who believe everything in the universe just happened to form by chance—decide it is a useless evolutionary leftover. Such a useless design is pressed into service as an evolution apologetic. Is not our useless and dangerous appendix yet another proof text of Darwinism? Later, when the function is eventually uncovered, evolutionists begrudgingly admit to it while maintaining that its clumsiness still proves evolution. As Richard Dawkins explained, in response to the growing knowledge of how well our “backward” retina works, “it is the principle of the thing that would offend any tidy-minded engineer!” Just because it works doesn’t mean it isn’t junk. And whatever function it luckily has is claimed as an evolutionary achievement—an obvious example of the power of natural selection.

Dan Graur’s entertaining talk on junk DNA, at the Society for Molecular Biology and Evolution this week, reminds us of this dynamic. The human genome must be full of junk DNA, indifferent DNA, garbage DNA and yes, Lazarus DNA (junk DNA that has gained some kind of function).

For our genome is small, low on genes, unoriginal and repetitive. Sure it is bigger than the genome of a bacteria and of the pufferfish, but it’s ten to a hundred times smaller than the lungfish and canopy plant genome.

If recent claims from the ENCODE project, that the human genome is mostly functional, turns out to be true, Graur points out, then the human genome would be the Goldilocks of biology. Not too hot, and not too cold (or in this case, not too small, and not too large). Just right.

ENCODE’s interpretation of the evidence must be wrong. In fact, if ENCODE isn’t wrong, then evolution is.

But ENCODE is wrong, the University of Houston molecular evolution expert concludes. Junk DNA is a known known.

And what is this evidence from ENCODE that our genome is mostly functional? It is that the cell’s copying machine, RNA polymerase, makes copies of it. But so what? Just because it is copied doesn’t mean it isn’t junk. What we have is not functional DNA but an over active, out-of-control copy machine. Apparently evolution’s natural selection didn’t mind this massive waste of cellular energy.

Perhaps so, but there is one glaring error in Graur’s otherwise excellent presentation. I assure you that the truth of evolution is not vulnerable to the status of junk DNA. Contrary to Graur, if ENCODE is right, that most assuredly will not mean that evolution is wrong.

If evolution can sustain the long history of false predictions that it has, then it will not be harmed by one more; namely, that there is more functional DNA than evolutionists would like. What is yet one more just-so story to a narrative so full of them?

Surely it won’t be a problem to explain that “Science has provided yet another surprise as we continue to learn how evolution worked. It turns out that most of the genome performs useful cellular functions, though as evolutionists point out, they are backwards and inefficient.”

Graur may or may not be correct that junk DNA is a known known, but for evolutionists, evolution is definitely a known known.

Thursday, July 11, 2013

The Dirty Dozen

If you like stories about a rag-tag group of misfits taking on the world then you’ll love evolution. As we discussed recently, evolutionists hold that the gene that codes for Xist, a long non coding RNA that performs a three-dimensional search for gene targets on the X-chromosome and helps to direct its inactivation, must have arisen from the merger of a few exons from a dead protein-coding gene, parts of a retrovirus, various mobile elements, and of course a bunch of mutations. This unlikely collection of collateral teamed up to lay down the design of a truly incredible RNA molecule. Perhaps that indeed occurred, but if so it would be quite serendipitous.

Tuesday, July 9, 2013

Wow

Genes in our DNA code for proteins, but those genes only account for a few percent of the entire genome. What is the rest of our DNA doing? Evolutionists thought it was mostly useless but, in fact, all kinds of functions have been implicated. Some of the DNA is transcribed in long segments but, unlike the coding genes, does not get translated into a protein. Instead, this large noncoding RNA (lncRNA) helps to regulate which protein-coding genes are transcribed. New research is helping to elucidate how lncRNA does its job. The findings are not only astonishing, they demolish evolutionary theory.

The new research studied a particular lncRNA, known as Xist, that directs X-chromosome inactivation. The researchers found that Xist performs a three-dimensional, spatial, search for key protein-coding genes and directs the rearrangement of the chromosome. The key genes, though far apart along the chromosome, are close together in the tangled chromosome structure and can be regulated as a single group by Xist. As one researcher explained:

You can now think about these lncRNAs as a way to bring together genes that are needed for common function into a single physical region and then regulate them as a set, rather than individually. They are not just scaffolds of proteins but actual organizers of genes.

So not only is the lncRNA DNA sequence important to perform its job, but its location and the locations of the other genes are important. And all of this depends on the intricate, three-dimensional structural details of the chromosome. As the researcher further explained:

LncRNAs, unlike proteins, really can use their genomic information—their context, their location—to act, to bring together targets. That makes them quite unique.

Indeed. Not only would random, chance mutations need somehow to luckily hit upon the lncRNA DNA sequence, but they would have to do that in the right place in the genome. And the chromosome structure, and location of the key genes and their packing proteins, need to support this incredible capability. Here is how one writer explained the findings:

Before Xist is activated, X-chromosome genes are all spread out. But, the researchers found, once Xist is turned on, it quickly pulls in genes, forming a cloud. “And it’s not just that the expression levels of Xist get higher and higher,” Guttman says. “It’s that Xist brings in all of these related genes into a physical nuclear structure. All of these genes then occupy a single territory.”

Evolution

The lncRNA’s function reveals that evolution is even more unlikely. Evolution is a theory of a large number of low probability events. Evolving the sequence is itself unlikely (evolutionists say it arose from mutations combining portions of a dead protein gene and mobile elements). Now those random mutations must do the job in the right place, within the genome, as well.

But that is not all. For lncRNAs such as Xist are not even well conserved across different species (it is not found outside the eutherians), as evolution predicts and expects. Such lack of sequence conservation, evolution predicts, should mean lack of function. But lncRNAs such as Xist obviously do not lack function.

This leaves evolutionists with nothing but yet another just-so story as their only alternative; namely, that lncRNAs such as Xist underwent “rapid evolution.”

Evolution predicts certain patterns to be found amongst the species, and when they find those patterns evolutionists proclaim them as proof of evolution. But when unique designs are found which contradict evolution’s expectations, which is far more prevalent than the textbooks reveal, evolutionists quietly explain them away as the results of “rapid evolution.” Here is how one paper explained the evolution of Xist:

The mammalian transcriptome contains many non-protein-coding RNAs (ncRNAs), but most of these are of unclear significance and lack strong sequence conservation, prompting suggestions that they might be non-functional. However, certain long functional ncRNAs such as Air and Xist are also poorly conserved. In this article, we systematically analyzed the conservation of several groups of functional ncRNAs, including miRNAs, snoRNAs and longer ncRNAs whose function has been either documented or confidently predicted. As expected, miRNAs and snoRNAs were highly conserved. By contrast, the longer functional non-micro, non-sno ncRNAs were much less conserved with many displaying rapid sequence evolution. Our findings suggest that longer ncRNAs are under the influence of different evolutionary constraints and that the lack of conservation displayed by the thousands of candidate ncRNAs does not necessarily signify an absence of function.

As highlighted above, this paper explains the lack of conservation, across species, of Xist and other lncRNAs, as a consequence of “rapid sequence evolution.” In fact, the paper goes further, making the non scientific claim that these lncRNAs display rapid sequence evolution.

That is, of course, a misrepresentation of the science. Resorting to an unfalsifiable, unlikely, explanation is one thing. It is even worse to present that explanation as a given. LncRNAs do not display rapid sequence evolution any more than a football field displays a flat Earth.

Ever since Darwin, evolutionists have required long time periods. Darwin was greatly concerned about Lord Kelvin’s arguments that the age of the Earth was limited to 100 million years. And evolutionists celebrated the resolution to those arguments and the upward revision of the Earth’s age into the billions of years. But when deep time is unavailable, such as with the origin of Xist, evolutionists simply enlist “rapid evolution.”

Did Xist evolve? Perhaps, perhaps not. Who knows what future research will reveal. But from a scientific perspective, the current evidence is abundantly clear. It is astronomically unlikely that Xist, with its amazing capabilities, evolved. The fact that it must have evolved “rapidly” adds an exclamation mark to the finding. An intricate sequence must have evolved with amazing functionality. Those random mutations must have evolved Xist in the right place within the genome. And all this must have happened rapidly, at the right time. The right sequence, the right place, and the right time. When it comes to science, evolutionary theory simply makes no sense.

Monday, July 8, 2013

Really?

Evolutionist Matt Ridley rightly pointed out last week that the scientific consensus does not exactly have a stellar track record:

There was once widespread agreement about phlogiston (a nonexistent element said to be a crucial part of combustion), eugenics, the impossibility of continental drift, the idea that genes were made of protein (not DNA) and stomach ulcers were caused by stress, and so forth—all of which proved false. Science, Richard Feynman once said, is “the belief in the ignorance of experts.”

So why is Ridley an evolutionist? “I agree with the majority view on evolution,” explains the British scientist and author, “not because it is a majority view but because I have looked at evidence. It’s the data that convince me, not the existence of a consensus.”

Looked at evidence? This reminds us of Thomas Huxley’s sentiment that one ought to “Sit down before fact as a little child, be prepared to give up every preconceived notion, follow humbly wherever and to whatever abysses nature leads.”

Every preconceived notion? Well not exactly. Not the preconceived notion that evolution must be true. Other than that, one can follow the evidence.

We can read in the genes exactly the whole history of life. And we’re gradually understanding all of that, and it absolutely confirms there’s descent with modification with natural selection, and all these things that Darwin said. There’s plenty of room for disagreement about the details. It’s not one dogmatic theory, there’s a whole bunch of theories.

The first thing they should do when they see a consensus is try and shoot it down. But there is no question that all creatures on this planet are [evolutionarily] related. We can see that in the genes. They all share the same genetic code—it looks like a frozen accident. There’s no rhyme or reason why we have the particular genetic code we do. But bacteria have it, we have it, plants have it—it’s all connected.

Exactly the whole history of life? no question?

Of course there are questions. And no, the genes do not reveal the whole history of life. Not if you don’t presuppose evolution to begin with. Yet Ridley is absolutely sure of himself. With evolution, the deviation from the evidence is exceeded only the certainty with which the theory is held.

Sunday, July 7, 2013

More Than Meets the Eye

Carl Sagan once responded to an evolution skeptic with a response that Sagan obviously had given some thought to. You can listen to the question and Sagan’s summary beginning at the [0:24] mark:

Skeptic: How do you explain the switch from asexual reproduction to sexual reproduction?

Sagan: First off, let me say that, that in no way challenges the validity of biological evolution, whether we’re able or unable to explain the fact that many species, by no means all, reproduce sexually today. The Darwinian concept of evolution and natural selection is profoundly verified, not just by the fossil record, not just by the clear experience of artificial selection, but by the record in the nucleic acids, which is obtained by DNA sequencing, in which we can see the similarities and differences of organisms, and trace their evolutionary past—their history.

Sagan begins by explaining that the failure to explain basic and important productions of evolution cannot challenge the validity of evolution. Philosophers call this theory-protectionism. If basic, important theoretical failures can do no harm, then the theory is not falsifiable.

Next Sagan provides three evidences for evolution: fossils, artificial selection and DNA comparisons. Even if all these evidences were as evolution predicted they would not prove evolution. In that case, Sagan’s claim that evolution is “profoundly verified” by these evidences amounts to the fallacy of affirming the consequent.

But it gets worse. For in all three cases, the evidence is not even what evolution expects, but instead contradicts the evolutionary prediction. The fossils do not form an evolutionary tree, but rather reveal abrupt diversity explosions followed by a winnowing due to extinctions. The expected evolutionary tree is turned upside down.

Likewise artificial selection, and the experience of breeders, reveals that species do not simply extrapolate indefinitely as evolution expects. Breeders can be bring about change, but only so much. Darwin had to say that natural selection had something that artificial selection did not. There is no evidence for that, but for our purposes that is irrelevant. The point is that artificial selection does not provide the evidence Sagan claimed it did.

Finally, like the fossil record, the DNA sequences also do not form an evolutionary tree, but instead contradict it. Evolutionists have to prefilter the sequence data, and perform several other intellectual twists, to force fit the data into a tree.

Saturday, July 6, 2013

Where Evolution Becomes Crystal Clear

Every once in a while evolutionists distill their thoughts into pithy statements that profoundly summarize what it’s all about for them. Carl Sagan’s 1980 Cosmos video is chocked full of such statements, but non better than his classic opening line: “The Cosmos is all that is, or ever was, or ever will be.” [Please click to see] Obviously that is a truth claim, but it does not come from science. Truth claims that do not come from science are nothing new. What is new, however, is the presentation of such truth as science. And so while there is nothing wrong with evolutionists proclaiming what they believe. There is everything wrong with their insistence that it is what everyone else must believe as well. That their personal religious beliefs, not open to scientific scrutiny, are scientific facts. Evolutionists may be correct about origins, but they are not scientific.

Here is a small, representative sampling of such claims over the past three centuries.

“We think him a better Artist that makes a Clock that strikes regularly at every hour from the Springs and Wheels which he puts in the work, than he that hath so made his Clock that he must put his finger to it every hour to make it strike.” Thomas Burnet, 1681

“Newton and his followers also have a very odd opinion regarding God’s workmanship. According to them, God’s watch—the universe—would stop working if he didn’t re-wind it from time to time! He didn’t have enough foresight to give it perpetual motion. This machine that he has made is so imperfect that from time to time he has to clean it by a miraculous intervention, and even has to mend it, as a clockmaker mends his work. The oftener a clockmaker has to adjust his machine and set it right, the clumsier he must be as a clockmaker!” Gottfried Leibniz, 1715

God would not “set his own hand as it were to every work, and immediately do all the meanest and trifling’st things himself drudgingly, without making use of any inferior or subordinate Minister.” John Ray, 1717

It is most appropriate to the wisdom of God that the cosmic structures “develop themselves in an unforced succession out of the universal laws.” Immanuel Kant, 1755

“A perpetual war is kindled amongst all living creatures,” and nature is so arranged so as “to embitter the life of every living being.” David Hume, 1779

“The world itself might have been generated, rather than created; that is, it might have been gradually produced from very small beginnings, increasing by the activity of its inherent principles, rather than by a sudden evolution by the whole by the Almighty fiat. What a magnificent idea of the infinite power of the great architect! The Cause of Causes! Parent of Parents! Ens Entium! For if we may compare infinities, it would seem to require a greater infinity of power to cause the causes of effects, than to cause the effects themselves.” Erasmus Darwin, 1794

“How can we suppose an immediate exertion of this creative power at one time to produce the zoophytes, another time to add a few marine mollusks, another to bring in one or two crustacea, again to crustaceous fishes, again perfect fishes, and so on to the end. This would surely be to take a very mean view of the Creative Power.” Robert Chambers, 1844

“No inductive inquirer can bring himself to believe in the existence of any real hiatus in the continuity of physical laws in past eras more than in the existing order of things; or to imagine that changes, however seemingly abrupt, can have been brought about except by the gradual agency of some regular causes. On such principles the whole superstructure of rational geology entirely reposes; to deny them in any instance would be to endanger all science. … The event [the introduction of new species] is part of a regularly ordained mechanism of the evolution of the existing world out of former conditions, and as much subject to regular laws as any changes now taking place.” Baden Powell, 1855

“these analogies are utterly inexplicable if species are independent creations.” Charles Darwin, 1859

“The strange springs and traps and pitfalls found in the flowers of Orchids cannot be necessary per se, since exactly the same end is gained in ten thousand other flowers which do not possess them. Is it not then an extraordinary idea to imagine the Creator of the Universe contriving the various complicated parts of these flowers as a mechanic might contrive an ingenious toy or a difficult puzzle? Is it not a more worthy conception that they are some of the results of those general laws which were so co-ordinated at the first introduction of life upon the earth as to result necessarily in the utmost possible development of varied forms?” –Alfred Wallace, 1870

“If whales were made at once out of hand as we now see them, is it conceivable that these useless teeth would have been given them?” –Joseph Le Conte, 1891

“What we do not know today we shall know tomorrow.” Alexander Oparin, 1924

“Odd arrangements and funny solutions are the proof of evolution—paths that a sensible God would never tread but that a natural process, constrained by history.” Stephen Jay Gould, 1980

“The Cosmos is all that is, or ever was, or ever will be.” Carl Sagan, 1980

Would God “really want to take credit for the mosquito?” Ken Miller, 1999

“There are too many deficiencies, too much cruelty in the world of life. To assume that they have been explicitly created by God amounts to blasphemy. I believe God to be omniscient and benevolent. The ‘design’ of organisms is not compatible with such beliefs.” Francisco Ayala, 2002

These claims are not from science, but they drive science. They determine what is acceptable and not acceptable. They inform science and constrain it the “right” answers. As was said so long ago, theology is the queen of the sciences. Imagine for a moment that you believed these things. Then you would be an evolutionist.

The Real Warfare Thesis

In his Computational Molecular Evolution course professor Anders Gorm Pedersen states that “evolutionary theory is the conceptual foundation of biology” and that “A phylogenetic [evolutionary] tree will almost always help you think more clearly about your biological problem.” That might seem strange since evolutionary theory’s fundamental predictions have turned out to be false and the species do not fit into an evolutionary tree. But all is clear when Pedersen approvingly quotes what is practically evolution’s official motto from Theodosius Dobzhansky: “Nothing in biology makes sense except in the light of evolution.”

This statement is diametrically opposed to empirical science, for it is a universal truth claim that is impossible in science. To better understand that you can first restate the motto to its logical positive equivalent: “Everything in biology only makes sense in light of evolution.” A scientist would never, and indeed could never, claim that evidence X can only be explained by theory Y. That’s because a scientist cannot know of all possible theories and explanations. Such knowledge simply is not available within science.

Aside from the minor problem that most of biology does not make sense in light of evolution (and that problem really is the minor one in this case), there is no scientific experiment or rationale that can inform us of all possible explanations for the origin of the world, let alone how well they explain the evidence.

But evolution never was about science in the first place. In evolutionary theory, the science is like window dressing. It comes after the fact that evolution is true. If you don’t believe me just read the literature. Dobzhansky’s non scientific statement is like a chant for evolutionists. It is the continual drumbeat in the background of evolutionary thought. It appears everywhere from the popular literature to peer-reviewed research papers to classroom material such as in Pedersen’s course.

Evolutionists could not be more clear about their beliefs and their non scientific claims. This is not a minor or tangential aspect of evolutionary thought. For evolutionists this is their core position. They are at war with empirical science. A theory that continually contradicts the evidence is declared to be a fact because, well, it must be.

Friday, July 5, 2013

More Moralizing

What is intriguing about evolution is not so much the idea itself but what comes along with the idea. Evolution’s idea—that the world arose spontaneously—is certainly enough to raise eyebrows since it goes against so much of what we know from science. But anti realism is not necessarily a bad thing in science, for science needs speculative ideas. What comes along with this particular speculative idea, however, is much more interesting and important. For evolutionists insist their idea is a fact. That claim—so at odds with the empirical evidence—indicates that there is something more to evolution than scientific theorizing. There is an underlying nonscientific foundation of evolution that mandates its certainty. This “fact” of evolution is, for evolutionists, so obvious and necessary that anyone who does not acknowledge it is, in their eyes, suspect. Evolutionists cannot understand how skeptics can have a legitimate argument—there must be ulterior motives at work. Skeptics must be up to no good. They are abusing science and they must be stopped. Evolutionists do not hesitate to cast aspersions on, judge and blackball skeptics. So along with the idea that the world arose strictly naturalistically, evolution brings epistemological and ethical claims which are as strongly held as they are unsupported. Unfortunately this combination of anti realism reinforced by moralizing seems to spreading.

Last week, in their ruling against the Defense of Marriage Act, the Supreme Court engaged in just this sort of moralizing. The court said that those who disagree with them are out to “disparage,” “injure,” “degrade,” “demean,” and “humiliate” our fellow human beings and citizens who are homosexual.

Of course the court holds no such monopoly on ethics. How could it when it did not even provide an alternative which the supposed bigots are to accept? Is one automatically a bigot for not agreeing to toss out the existing definition of marriage when no alternative is offered and to solve a tax problem?

One may agree or disagree with the existing definition of marriage, and that definition may change in the future as society sees fit. But erroneous blanket accusations of bigotry do not advance the discussion and are reminiscent of how evolutionists argue for their theory.

When we pointed this out evolutionists doubled down on their moralizing. Rather than realize the fallacy, they insisted that even our mere pointing this out, itself, constitutes bigotry. In other words, regardless of one’s position on the issue of marriage, acknowledging any legitimacy to the existing definition constitutes bigotry. Amazing.

This sort of hyper critical judgment is typical of evolutionists. The evolutionist’s combination of certainty and self-righteous moralizing is toxic to reasoned debate. Unfortunately it seems to be spreading.